- The sorrow in Iji's voice after her first few kills. "I'm sorry..."
- The hair ribbons scattered through the complex that belonged to Iji's now-dead sister, is really makes it clear just how much Iji has lost due to the Tasen, especially when Iji realizes she's been hallucinating them.
- If the player fails to obtain or take heed of the warning Iji senses from the hair ribbons, and the player similarly fails to exhibit precognition, Asha kills Iji's brother and Iji suffers a Heroic BSoD and goes on talking to him as if he's still alive.
- The last stand of the Tasen. It's bad enough watching them be hunted down and slaughtered one by one by the deeply sociopathic Komato if you've been reading the various logbooks, but when they're driven to their very last holdout the conclusion is all the more painful because the Tasen diary writer and her girlfriend, and Vateilika, if they're still alive, are all holing up there, and if you've been on the violent path, before you can enter something tears through their defenses and butchers them all.
- The ending and the death of General Tor is very heartbreaking.
- ESPECIALLY the ending in which you don't save Dan from Asha. The entire planet is almost devoid of life, save for ants and plants, and the few humans, Dan is dead, and the Tasen are on the verge of extinction, if not extinct already.
- The song used in the credits, "Further", originally by VNV Nation but the version used in the game is a cover by Life Force. While it wasn't written specifically for this game like the rest of the soundtrack, it might as well have been. The lyrics pretty much describe Iji's view of the entire conflict, and if you think of it as if she's singing to Tor after he dies, it becomes that much more powerful.
- Version 1.7 adds a new ending if you choose to be particularly violent, and it is in no way positive. After the battle with Tor a prompt appears to kill him before he can say anything. Do so, and Kiron chimes in on the communicator to explain that Tor was testing you to see if humanity was worth saving, and to chew Iji out for killing the only person willing to actually listen to her. He then orders the Alpha Strike to fire, and Iji can only tearfully hug Dan (if Asha hasn't kill him already) before it destroys the Earth.
- There's still yet a THIRD ending that, while not as bad, is still very bittersweet. Instead of a cutscene playing, you now personally have to pull the trigger to kill Iosa and Tor. If you try to merely kick Iosa to knock her out, she will not repay your kindness. She is awakened by a Berserker who she demands fetch her gun, a generation 2 gun that is illegal to use in active combat because of how hideously devastating its arsenal can get to prevent it from being reverse-engineered. After you beat Tor, she arrives to decisively and finally kill Iji. She then tries to extort Tor into Alpha Striking the planet, sensing weakness within him, only to be reprimanded by Kiron, stripped of her rank, and having Tor call off the strike anyway. She kills Tor in a rage since she's already been punished, and storms back onto a ship as the fleet leaves. Dan, if he's even alive, is left to look at the fleet taking off after his sister died to ensure it happened. As they leave the planet, Iosa just stares at her hands in disbelief as she realizes she just killed not only a completely innocent combatant, but her own husband over the idea of being denied her vengeance.
- Another feature added in version 1.7: the room before the final boss now contains two logbooks detailing the name, rank, birthplace, and (in certain cases) cause of death (even fruit-assisted for Black Comedy or Crosses the Line Twice) of every single Tasen and Komato that Iji personally killed. The number of entries can be anywhere from zero to over three hundred, and these logbooks serve as a reminder that every one of them was an individual. And, on a more Nightmare Fuel-y note, the entries for Beasts list not "Born", but "Converted".
Tear Jerker / Iji